New api, to easily use VisTrails in other applications

vistrails/__init__.py

@@ -53,3 +53,6 @@
     sys.stderr.write("WARNING: Your unittest is missing 2.7 features. Please "
                      "upgrade Python or\ninstall unittest2, else VisTrails "
                      "might fail because of missing symbols.\n")
+
+
+from vistrails.core.api import *

vistrails/core/configuration.py

@@ -86,6 +86,7 @@
 jobCheckInterval: How often to check for jobs (in seconds)
 jobList: List running workflows
 jobInfo: List jobs in running workflow
+loadPackages: Whether to load the packages enabled in the configuration file
 logDir: Log files directory
 maxRecentVistrails: Number of recent vistrails
 maximizeWindows: VisTrails windows should be maximized
@@ -251,6 +252,10 @@
 
     List jobs in running workflow
 
+loadPackages: Boolean
+
+    Whether to load the packages enabled in the configuration file
+
 logDir: Path
 
     The path that indicates where log files should be stored.
@@ -702,6 +707,7 @@ def __init__(self, name, sub_fields):
          ConfigField('cacheSize', 20, int, widget_type='thumbnailcache')])],
     "Packages":
     [ConfigField('enablePackagesSilently', False, bool, ConfigType.ON_OFF),
+     ConfigField('loadPackages', True, bool, ConfigType.ON_OFF),
      ConfigField('installBundles', True, bool, ConfigType.ON_OFF),
      ConfigField('installBundlesWithPip', False, bool, ConfigType.ON_OFF,
                  depends_on="installBundles"),

vistrails/core/modules/basic_modules.py

@@ -52,6 +52,7 @@
 from abc import ABCMeta
 from ast import literal_eval
 from itertools import izip
+import mimetypes
 import os
 import pickle
 import re
@@ -332,14 +333,35 @@ def query_compute(value_a, value_b, query_method):
 
 ##############################################################################
 
+# Rich display for IPython
+try:
+    from IPython import display
+except ImportError:
+    display = None
+
 class PathObject(object):
     def __init__(self, name):
         self.name = name
+        self._ipython_repr = None
 
     def __repr__(self):
         return "PathObject(%r)" % self.name
     __str__ = __repr__
 
+    def __getattr__(self, name):
+        if name.startswith('_repr_') and name.endswith('_'):
+            if self._ipython_repr is None:
+                filetype, encoding = mimetypes.guess_type(self.name)
+                if not filetype:
+                    self._ipython_repr = False
+                elif filetype.startswith('image/'):
+                    self._ipython_repr = display.Image(filename=self.name)
+                else:
+                    self._ipython_repr = False
+            elif self._ipython_repr is not False:
+                return getattr(self._ipython_repr, name)
+        raise AttributeError
+
 class Path(Constant):
     _settings = ModuleSettings(constant_widget=("%s:PathChooserWidget" % \
                                                 constant_config_path))

vistrails/core/modules/output_modules.py

@@ -504,10 +504,45 @@ class ImageFileMode(FileMode):
     config_cls = ImageFileModeConfig
     mode_type = "imageFile"
 
+class IPythonModeConfig(OutputModeConfig):
+    mode_type = "ipython"
+    _fields = []
+
+class IPythonMode(OutputMode):
+    mode_type = "ipython"
+    priority = 2
+    config_cls = IPythonModeConfig
+
+    @staticmethod
+    def can_compute():
+        try:
+            import __main__ as main
+            if hasattr(main, '__file__'):
+                return False
+            import IPython.core.display
+            return True
+        except ImportError:
+            return False
+
+    def compute_output(self, output_module, configuration=None):
+        from IPython.core.display import display
+
+        value = output_module.get_input('value')
+        display(value)
+
+class IPythonHtmlMode(IPythonMode):
+    mode_type = "ipython"
+
+    def compute_output(self, output_module, configuration=None):
+        from IPython.core.display import display, HTML
+
+        value = output_module.get_input('value')
+        display(HTML(filename=value.name))
+
 class RichTextOutput(OutputModule):
     _settings = ModuleSettings(configure_widget="vistrails.gui.modules.output_configuration:OutputModuleConfigurationWidget")
     _input_ports = [('value', 'File')]
-    _output_modes = [FileToFileMode]
+    _output_modes = [FileToFileMode, IPythonHtmlMode]
 
 _modules = [OutputModule, GenericOutput, FileOutput, RichTextOutput]
 

vistrails/core/packagemanager.py

@@ -47,14 +47,14 @@
 import warnings
 
 from vistrails.core import debug, get_vistrails_application, system
-from vistrails.core.configuration import ConfigurationObject
+from vistrails.core.configuration import ConfigurationObject, \
+    get_vistrails_configuration
 import vistrails.core.data_structures.graph
-import vistrails.core.db.io
-from vistrails.core.modules.module_registry import ModuleRegistry, \
-                                         MissingPackage, MissingPackageVersion
+from vistrails.core.modules.module_registry import MissingPackage, \
+    MissingPackageVersion
 from vistrails.core.modules.package import Package
 from vistrails.core.requirements import MissingRequirement
-from vistrails.core.utils import VistrailsInternalError, InstanceObject, \
+from vistrails.core.utils import VistrailsInternalError, \
     versions_increasing, VistrailsDeprecation
 import vistrails.packages
 
@@ -124,7 +124,6 @@ def import_user_packages_module(self):
         if self._userpackages is not None:
             return self._userpackages
         # Imports user packages directory
-        conf = self._startup.temp_configuration
         old_sys_path = copy.copy(sys.path)
         userPackageDir = system.get_vistrails_directory('userPackageDir')
         if userPackageDir is not None:
@@ -183,8 +182,23 @@ def __init__(self, registry, startup):
         # Compute the list of available packages, _available_packages
         self.build_available_package_names_list()
 
-        for pkg in self._startup.enabled_packages.itervalues():
-            self.add_package(pkg.name, prefix=pkg.prefix)
+        if get_vistrails_configuration().loadPackages:
+            for pkg in self._startup.enabled_packages.itervalues():
+                self.add_package(pkg.name, prefix=pkg.prefix)
+        else:
+            try:
+                basic_pkg = self._startup.enabled_packages['basic_modules']
+            except KeyError:
+                pass
+            else:
+                self.add_package(basic_pkg.name, prefix=basic_pkg.prefix)
+
+            try:
+                abs_pkg = self._startup.enabled_packages['abstraction']
+            except KeyError:
+                pass
+            else:
+                self.add_package(abs_pkg.name, prefix=abs_pkg.prefix)
 
     def _import_override(self,
                          name, globals={}, locals={}, fromlist=[], level=-1):

vistrails/core/vistrail/controller.py

@@ -2605,10 +2605,10 @@ def execute_workflow_list(self, vistrails):
                     extra_info = {}
                 extra_info['pathDumpCells'] = create_temp_folder(prefix='vt_thumb')
                 temp_folder_used = True
-#           
+
             kwargs = {'locator': locator,
                       'current_version': version,
-                      'view': view,
+                      'view': view if view is not None else DummyView(),
                       'logger': self.get_logger(),
                       'controller': self,
                       'aliases': aliases,
@@ -2706,12 +2706,11 @@ def execute_current_workflow(self, custom_aliases=None, custom_params=None,
                 locator.clean_temporaries()
                 if self._auto_save:
                     locator.save_temporary(self.vistrail)
-            view = DummyView()
             try:
                 return self.execute_workflow_list([(self.locator,
                                                     self.current_version,
                                                     self.current_pipeline,
-                                                    view,
+                                                    None,
                                                     custom_aliases,
                                                     custom_params,
                                                     reason,
@@ -2790,7 +2789,7 @@ def recompute_terse_graph(self):
         self._current_terse_graph = tersedVersionTree
         self._current_full_graph = self.vistrail.tree.getVersionTree()
 
-    def save_version_graph(self, filename, tersed=True):
+    def save_version_graph(self, filename, tersed=True, highlight=None):
         if tersed:
             graph = copy.copy(self._current_terse_graph)
         else:
@@ -2806,7 +2805,13 @@ def save_version_graph(self, filename, tersed=True):
         configuration = get_vistrails_configuration()
         use_custom_colors = configuration.check('enableCustomVersionColors')
 
-        with open(filename, 'wb') as fp:
+        if isinstance(filename, basestring):
+            fp = open(filename, 'wb')
+            cleanup = lambda: fp.close()
+        else:
+            fp = filename
+            cleanup = lambda: None
+        try:
             fp.write('digraph G {\n')
             for v in vs:
                 descr = tm.get(v, None) or self.vistrail.get_description(v)
@@ -2821,15 +2826,20 @@ def save_version_graph(self, filename, tersed=True):
                             '%02x' % c
                             for c in parse_custom_color(color.value))
                     fp.write('    %s [label=%s, '
-                             'style=filled, fillcolor="%s"];\n' % (
-                             v, dot_escape(descr), color))
+                             'style=filled, fillcolor="%s", color="%s"];\n' % (
+                             v, dot_escape(descr), color,
+                             'red' if v == highlight else 'black'))
                 else:
-                    fp.write('    %s [label=%s];\n' % (v, dot_escape(descr)))
+                    fp.write('    %s [label=%s, color="%s"];\n' % (
+                             v, dot_escape(descr),
+                             'red' if v == highlight else 'black'))
             fp.write('\n')
             for s in al:
                 vfrom, vto, vdata = s
                 fp.write('    %s -> %s;\n' % (vfrom, vto))
             fp.write('}\n')
+        finally:
+            cleanup()
 
     def get_latest_version_in_graph(self):
         if not self._current_terse_graph:

vistrails/packages/matplotlib/bases.py

@@ -34,18 +34,16 @@
 
 from __future__ import division
 
-import itertools
-import matplotlib
-from matplotlib.backend_bases import FigureCanvasBase
 import pylab
 import urllib
 
 from matplotlib.backend_bases import FigureCanvasBase
 
+from vistrails.core.configuration import ConfigField
 from vistrails.core.modules.basic_modules import CodeRunnerMixin
 from vistrails.core.modules.config import ModuleSettings, IPort
 from vistrails.core.modules.output_modules import ImageFileMode, \
-    ImageFileModeConfig, OutputModule
+    ImageFileModeConfig, OutputModule, IPythonModeConfig, IPythonMode
 from vistrails.core.modules.vistrails_module import Module, NotCacheable
 
 ################################################################################
@@ -146,18 +144,37 @@ def compute_output(self, output_module, configuration=None):
         figure.set_size_inches(previous_size[0],previous_size[1])
         canvas.draw()
 
+class MplIPythonModeConfig(IPythonModeConfig):
+    mode_type = "ipython"
+    _fields = [ConfigField('width', None, int),
+               ConfigField('height', None, int)]
+
+class MplIPythonMode(IPythonMode):
+    mode_type = "ipython"
+    priority = 2
+    config_cls = MplIPythonModeConfig
+
+    def compute_output(self, output_module, configuration=None):
+        from IPython.display import set_matplotlib_formats
+        from IPython.core.display import display
+
+        set_matplotlib_formats('png')
+
+        # TODO: use size from configuration
+        fig = output_module.get_input('value')
+        display(fig.figInstance)
+
 class MplFigureOutput(OutputModule):
     _settings = ModuleSettings(configure_widget="vistrails.gui.modules.output_configuration:OutputModuleConfigurationWidget")
     _input_ports = [('value', 'MplFigure')]
-    _output_modes = [MplFigureToFile]
+    _output_modes = [MplFigureToFile, MplIPythonMode]
 
 _modules = [(MplProperties, {'abstract': True}),
-            (MplPlot, {'abstract': True}), 
+            (MplPlot, {'abstract': True}),
             (MplSource, {'configureWidgetType': \
                              ('vistrails.packages.matplotlib.widgets',
                               'MplSourceConfigurationWidget')}),
             MplFigure,
             MplContourSet,
             MplQuadContourSet,
             MplFigureOutput]
-

vistrails/packages/tabledata/common.py

@@ -7,7 +7,8 @@
 
 from vistrails.core.modules.basic_modules import List, ListType
 from vistrails.core.modules.config import ModuleSettings
-from vistrails.core.modules.output_modules import OutputModule, FileMode
+from vistrails.core.modules.output_modules import OutputModule, FileMode, \
+    IPythonMode
 from vistrails.core.modules.vistrails_module import Module, ModuleError, \
     Converter
 
@@ -279,9 +280,7 @@ def compute(self):
                 ['converted_list']))    # names
 
 
-class TableToFileMode(FileMode):
-    formats = ['html', 'csv']
-
+class HtmlRendererMixin(object):
     @staticmethod
     def make_html(table):
         document = ['<!DOCTYPE html>\n'
@@ -316,6 +315,10 @@ def make_html(table):
 
         return ''.join(document)
 
+
+class TableToFileMode(FileMode, HtmlRendererMixin):
+    formats = ['html', 'csv']
+
     def write_html(self, table, configuration):
         filename = self.get_filename(configuration, suffix='.html')
         with open(filename, 'wb') as fp:
@@ -338,10 +341,19 @@ def compute_output(self, output_module, configuration=None):
             func(value, configuration)
 
 
+class TableToIPythonMode(IPythonMode, HtmlRendererMixin):
+    def compute_output(self, output_module, configuration=None):
+        from IPython.core.display import display, HTML
+
+        table = output_module.get_input('value')
+        html = self.make_html(table)
+        display(HTML(data=html))
+
+
 class TableOutput(OutputModule):
     _settings = ModuleSettings(configure_widget="vistrails.gui.modules.output_configuration:OutputModuleConfigurationWidget")
     _input_ports = [('value', 'Table')]
-    _output_modes = [TableToFileMode]
+    _output_modes = [TableToFileMode, TableToIPythonMode]
 
 
 _modules = [(Table, {'abstract': True}), ExtractColumn, BuildTable,